One of the most ravaging diseases of the late twentieth century has been acquired immunodeficiency syndrome (AIDS), caused by infection with HIV. There are several known strains of HIV including HIV-1, a collective term referring to several strains isolated in Europe or America, and HIV-2, a strain endemic in many West African countries. HIV-1 is classified by phylogenetic analysis into three groups, group M (major), group O (outlier) and a new variant of HIV-1, designated group N, that has been identified with its epicenter in Cameroon (Simon et al., Nat Med 4:1032-1037 (1998)). All three HIV-1 groups cause AIDS.
Group M contains at least ten subtypes, referred to as A through J, based on the sequence heterogeneity of the envelope region. Group O includes most divergent viruses that do not cluster with group M strains. Group N includes viruses that are distinct from HIV-1 groups M and O. For example, detailed genetic analyses have placed the origin of the YBF30 virus of group N far from that of group O, somewhere between group M and simian immunodeficiency virus (SIV) cpz-gabs. The worldwide distribution of various group M HIV-1 subtypes is diverse, with subtype B being most prevalent in North America and Europe and subtype A being most prevalent in Africa. Whereas most subtypes are common in Central Africa, other areas have restricted distribution of genotypes; for instance subtype E is highly prevalent in Thailand, subtype C is common in India and South Africa, and subtype F is prevalent in Romania, Brazil and Argentina. Type O infections have been identified in the West Central African countries of Cameroon and neighboring countries, such as Equatorial Guinea and Gabon. The spread of group O infections to Europe and more recently to the United States has been documented, although all patients have had links to West Central Africa.
The wide divergence of the HIV-1 group O viruses has created serious public health concerns regarding the safety of the blood supply. Reports by Eberle et al., J. Virol. Methods 67:85-91 (1997), and Loussert-Ajaka et al., J. Virol. 69:5640-5649 (1995) have indicated that serologic screening assays based on group M viruses, such as HIV-1 subtype B-based assays, may be unable to consistently detect group O infected blood. The residual risk of HIV-transmission from transfusions of blood screened using current antibody and antigen tests is estimated by scientists such as Schreiber et al., New Engl. J. of Med. 334:1685 (1996), to be two blood donations per million in the United States. The prevalence of group O infections in Africa and the spread of type O infections to other continents emphasizes the need for improved screening of the international blood supply. Ideally, improved screening assays should be highly sensitive in detecting all variants of HIV-1 group M, N and O contamination in donor blood. In addition, the screening assays should be able to detect plasma viremia, thereby allowing for earlier detection of HIV-1 and reducing blood transfusion infections associated with “window period” cases in which an individual is infected with the virus, but has not yet produced detectable levels of antibody against the virus.
Most commercially available HIV diagnostic assays are based on the detection of anti-HIV antibodies and antigens. However, several reports have shown that antibodies against some variants of HIV-1 group O are not reliably detected by these assays, primarily due to diversity in the immunodominant regions of HIV-1. If undiagnosed, these HIV-infected individuals may engage in activities or conduct resulting in the spread of the virus. In addition, these undiagnosed individuals may remain untreated, allowing the disease to progress until the onset of immunodeficiency symptoms.
Some of the currently available HIV diagnostic tests and many of the viral load assay tests used to assess the success of therapeutic treatment are nucleic acid-based. (Respess et al., J. Clin. Microbiol. 35:1284-1286 (1997)). Scientists have reported that these nucleic acid-based assays exhibit reduced sensitivities for non-subtype B HIV isolates (Alaeus et al., AIDS 11:859-865 (1997)). Since therapeutic regimens are evaluated and monitored by analyzing viral loads, the inability of current assays to accurately quantitate the viral load of all subtypes is a detriment to successful therapy (Cavert, AIDS12 (Suppl. A): S27 (1998)).
While several molecular detection assays have been described for the detection of proviral DNA from peripheral blood (Respess et al, J. Clin. Micro. 35:1284-1286 (1997); Fransen et al., Mol. Cellular Probes 8:317-322 (1994); Loussert-Ajaka et al., Lancet 346:912-913 (1995)), none can amplify both group M and O HIV-1 strains from plasma using a single assay.
Therefore, what are needed are methods for detecting group M, N and O HIV infections in blood plasma, serum or other biological samples using a single assay and methods for distinguishing between group M, N and O infections in biological samples. In addition, highly sensitive qualitative and quantitative assays for HIV-1 group M, N and O viruses are needed.